RetrogeneDB ID: retro_dnov_2369

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_67886:40388..40984(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SLC25A33
• Ensembl ID: ENSDNOG00000014396
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier), member 33 [Source:HGNC Symbol;Acc:29681]

Sequence

>retro_dnov_2369
CCTAAGAACAACATTGTGCACATTTTCTCAGCTGGCTCTGCAGCTTTTGTCACAAATTCCTTAATGAATTTATTTGGATG
GTTAAAACCCGGATGCAGCTAGAAGGGAGAATAAGAGGCTCCAAGCAAATGAATACACTCCAGTGTGCTCGCTATGTTTA
CCGGACAGAAGGCATCCGGGGCTTCTACAGAGGACTAACTGCCTCGTATGCTGGGATTTCAGAAACTATAATCTGTTTTG
CTATTTATGAAAGTTTAAAGAAGTATCTGAAAGAAGGTCCATTAGCCTCTTCTACAAATGGGACTGAGAAAAATTCCACA
AATTTTTTTGGACTCATGGCAGCTGCTGCCTTCTCTAAGGGATGTGCCTCCTGCATTGCTTATCCACATGAAGTCATAAG
GACACGGCTCCGTGAGGAAGGCACCAAGTACAAGTCTTTCATCCAGACCGCTCGCCTGGTGTTCCGGGAAGAAGGCTATC
TTGCCTTTTTATAGAGGACTTTTTTGCCCAGCTCATCAGGCAGATTCCAAAATACTGCCATTGTGTTGGTCTACCTATGA
GTTAATTGTGGTACCTGTTTGGAAGACCATATTCAG

Alignment

ORF - retro_dnov_2369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.61 %
• Parental protein coverage: 65.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PNSNVVHIFSAGSAAFVTNSLMNP-IWMVKTRMQLEGRIRGSKQMNTLQCARYVYRTEGIRGFYRGLTAS
          P..N.VHIFSAGSAAFVTNSLMN..IWMVKTRMQLEGRIRGSKQMNTLQCARYVYRTEGIRGFYRGLTAS
Retrocopy PKNNIVHIFSAGSAAFVTNSLMNL<IWMVKTRMQLEGRIRGSKQMNTLQCARYVYRTEGIRGFYRGLTAS

Parental  YAGISETIICFAIYESLKKYLKEGPLASSTNGTEKNSTNFFGLMAAAAFSKGCASCIAYPHEVIRTRLRE
          YAGISETIICFAIYESLKKYLKEGPLASSTNGTEKNSTNFFGLMAAAAFSKGCASCIAYPHEVIRTRLRE
Retrocopy YAGISETIICFAIYESLKKYLKEGPLASSTNGTEKNSTNFFGLMAAAAFSKGCASCIAYPHEVIRTRLRE

Parental  EGTKYKSFIQTARLVFREEGYLAF-YRGL-FAQLIRQIP-NTAIVL-STYELIV-YL-LEDHIQ
          EGTKYKSFIQTARLVFREEGYLAF.YRGL.FAQLIRQIP.NTAIVL.STYELIV.YL.LEDHIQ
Retrocopy EGTKYKSFIQTARLVFREEGYLAF>YRGL>FAQLIRQIP>NTAIVL>STYELIV>YL>LEDHIQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.39 RPM	6.22 RPM
SRP012922_cerebellum	0.14 RPM	12.37 RPM
SRP012922_heart	0.46 RPM	20.65 RPM
SRP012922_kidney	0.27 RPM	25.19 RPM
SRP012922_liver	0.00 RPM	4.64 RPM
SRP012922_lung	0.15 RPM	5.19 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.87 RPM
SRP012922_spleen	0.11 RPM	7.21 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_2369 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000424	1 retrocopy	retro_cjac_2186,
Dasypus novemcinctus	ENSDNOG00000014396	1 retrocopy	retro_dnov_2369 ,
Homo sapiens	ENSG00000171612	1 retrocopy	retro_hsap_873,
Gorilla gorilla	ENSGGOG00000006766	1 retrocopy	retro_ggor_709,
Monodelphis domestica	ENSMODG00000003059	1 retrocopy	retro_mdom_1512,
Otolemur garnettii	ENSOGAG00000007103	1 retrocopy	retro_ogar_2098,